diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index 65b41a82c..7b57058c6 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -245,17 +245,8 @@ public class GenomeAnalysisTK extends CommandLineProgram {
                     Utils.scareUser(String.format("Analysis %s doesn't support SAM/BAM reads, but a read file %s was provided", Analysis_Name, INPUT_FILES));
 
                 if ( WALK_ALL_LOCI ) {
-                    // TODO: Temporary debugging code.  Activate the new debugging code only when the MicroScheduler
-                    //                                  is not filtered.
-                    if( !DISABLE_THREADING ) {
-                        logger.warn("Preliminary threading support ENABLED");
-                        microScheduler = MicroScheduler.create( walker, INPUT_FILES, REF_FILE_ARG, rods, numThreads );
-                        this.engine = microScheduler.getTraversalEngine();
-                    }
-                    else {
-                        logger.warn("Preliminary threading support DISABLED");
-                        this.engine = new TraverseByLociByReference(INPUT_FILES, REF_FILE_ARG, rods);
-                    }
+                    microScheduler = MicroScheduler.create( walker, INPUT_FILES, REF_FILE_ARG, rods, numThreads );
+                    this.engine = microScheduler.getTraversalEngine();
                 }
                 else
                 	this.engine = new TraverseByLoci(INPUT_FILES, REF_FILE_ARG, rods);
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java
deleted file mode 100644
index 83f3c808f..000000000
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java
+++ /dev/null
@@ -1,122 +0,0 @@
-package org.broadinstitute.sting.gatk.traversals;
-
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
-import org.broadinstitute.sting.gatk.iterators.LocusIteratorByHanger;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-
-import java.util.List;
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.ArrayList;
-import java.io.File;
-
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.util.CloseableIterator;
-import edu.mit.broad.picard.filter.FilteringIterator;
-
-/**
- * A simple, short-term solution to iterating over all reference positions over a series of
- * genomic locations. Simply overloads the superclass traverse function to go over the entire
- * interval's reference positions.
- */
-public class TraverseByLociByReference extends TraverseByLoci {
-
-    public TraverseByLociByReference(List<File> reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
-        super(reads, ref, rods);
-    }
-
-    public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
-        //if ( locations.isEmpty() )
-        //    Utils.scareUser("Requested all locations be processed without providing locations to be processed!");
-
-        return super.traverse(walker, locations);
-    }
-
-    protected <M, T> T carryWalkerOverInterval( LocusWalker<M, T> walker,
-                                                Iterator<SAMRecord> readIter,
-                                                T sum,
-                                                GenomeLoc interval ) {
-        logger.debug(String.format("TraverseByLociByReference.carryWalkerOverInterval Genomic interval is %s", interval));
-
-        boolean done = false;
-
-        List<SAMRecord> NO_READS = new ArrayList<SAMRecord>();
-        List<Integer> NO_OFFSETS = new ArrayList<Integer>();
-
-        FilteringIterator filterIter = new FilteringIterator(readIter, new locusStreamFilterFunc());
-        LocusIterator locusIter = new LocusIteratorByHanger(filterIter);        // prepare the iterator by loci from reads
-
-        ReferenceIterator refSite = null;
-        LocusContext locusFromReads = null;
-
-        if( interval != null ) {
-            refSite = refIter.seekForward(interval);              // jump to the first reference site
-            locusFromReads = advanceReadsToLoc(locusIter, interval);    // load up the next locus by reads
-        }
-        else {
-            refSite = refIter.next();
-            locusFromReads = locusIter.next();
-        }
-
-        // We keep processing while the next reference location is within the interval
-        while ( (interval == null || interval.containsP(refSite.getLocation())) && ! done ) {
-            logger.debug(String.format("  LocusFromReads is %s", locusFromReads == null ? null : locusFromReads.getLocation()));
-
-            TraversalStatistics.nRecords++;
-            GenomeLoc current = refSite.getLocation();
-            
-            // Iterate forward to get all reference ordered data covering this locus
-            final RefMetaDataTracker tracker = getReferenceOrderedDataAtLocus(current);
-
-            LocusContext locus = null;
-
-            if ( locusFromReads != null && locusFromReads.getLocation().compareTo(current) == 0 ) {   // we are at the same site
-                locus = locusFromReads;
-                if ( locusIter.hasNext() )
-                    locusFromReads = locusIter.next();                          // advance the iterator
-            }
-            else
-                locus = new LocusContext(current, NO_READS, NO_OFFSETS);    // make the empty locus that has no reads
-
-            locus.setReferenceContig(refSite.getCurrentContig());            
-            if ( DOWNSAMPLE_BY_COVERAGE )
-                locus.downsampleToCoverage(downsamplingCoverage);
-            sum = walkAtLocus( walker, sum, locus, refSite, tracker );
-
-            if (this.maxReads > 0 && TraversalStatistics.nRecords > this.maxReads) {
-                logger.warn(String.format("Maximum number of reads encountered, terminating traversal " + TraversalStatistics.nRecords));
-                done = true;
-            }
-            
-            printProgress("loci", locus.getLocation());
-            refSite = refIter.next();                                       // update our location
-        }
-
-        return sum;
-    }
-
-
-    private LocusContext advanceReadsToLoc(LocusIterator locusIter, GenomeLoc target) {
-        if ( ! locusIter.hasNext() )
-            return null;
-        
-        LocusContext locus = locusIter.next();
-
-        while ( ! target.containsP(locus.getLocation()) && locusIter.hasNext() ) {
-            logger.debug(String.format("  current locus is %s vs %s => %d", locus.getLocation(), target, locus.getLocation().compareTo(target)));
-            locus = locusIter.next();
-        }
-
-        logger.debug(String.format("  returning %s", locus.getLocation()));
-        return locus;
-    }
-}
\ No newline at end of file